From 41d578f786c75f63f508dbc9828f89b5a1c3ba8a Mon Sep 17 00:00:00 2001
From: niyarin <inoanet@gmail.com>
Date: Tue, 18 Jul 2023 16:27:48 +0900
Subject: [PATCH] Fix some validate-error mesages and coding styles.

---
 src/cljam/io/vcf/util/validator.clj       | 18 ++++++++++--------
 test/cljam/io/vcf/util/validator_test.clj |  7 ++++---
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/cljam/io/vcf/util/validator.clj b/src/cljam/io/vcf/util/validator.clj
index 377a0de1..fed45d98 100644
--- a/src/cljam/io/vcf/util/validator.clj
+++ b/src/cljam/io/vcf/util/validator.clj
@@ -71,11 +71,11 @@
         type-check
         (conj
          (format
-          "Not match type declaration. Requires %s , but %s."
+          "Not match type declaration. Requires %s, but got %s."
           type (str entries)))
         number-check
         (conj
-         (format "Invalid number of elements. Requires %s , but %d."
+         (format "Invalid number of elements. Requires %s, but got %d."
                  (str number) (count entries)))))))
 
 (defn- check-each-samples [variant samples mformat]
@@ -100,7 +100,7 @@
   #(or (nil? %) ((set (map (comp keyword :id) format)) %)))
 
 (defn- make-info-validator [meta-info]
-  (let [id->info (map (comp keyword :id) meta-info)]
+  (let [id->info (into {} (map (juxt (comp keyword :id) identity)) meta-info)]
     (fn [info alt-num]
       (reduce
        (fn [validated [id entry]]
@@ -131,13 +131,15 @@
   ((make-validator* meta-info header) variant))
 
 (defn validate-variants
-  "Takes a variants list and throws an illegal variant
-  if it contains illegal content.
-  If there are no illegal mutations, the input list is returned as-is.
-  Validation is delayed."
+  "Checks if there is any invalid variant in the given sequence `variants`.
+  The validity of a variant is defined by `meta-info` and `header`.
+  Returns a lazy sequence of the same elements of the input if there are no
+  invalid variant. The validation is evaluated lazily and throws an exception
+  at the first invalid variant."
   [meta-info header variants]
   (let [validator (make-validator* meta-info header)]
     (map (fn [v]
            (when-let [info (validator v)]
-             (throw (ex-info "Invalid variant." (assoc info :variant v))))
+             (throw (ex-info (str "VCF validatoin failed: " (keys info))
+                             (assoc info :variant v))))
            v) variants)))
diff --git a/test/cljam/io/vcf/util/validator_test.clj b/test/cljam/io/vcf/util/validator_test.clj
index 7b206dd0..13e7ea3c 100644
--- a/test/cljam/io/vcf/util/validator_test.clj
+++ b/test/cljam/io/vcf/util/validator_test.clj
@@ -18,7 +18,8 @@
                     {:normal {:DP "str100"}} [:normal]
                     {:DP {:type "Integer" :number 1}})
                    [:normal :DP])
-           ["Not match type declaration. Requires Integer , but [\"str100\"]."]))
+           [(str "Not match type declaration. "
+                 "Requires Integer, but got [\"str100\"].")]))
     (is (nil?
          (#'validator/check-each-samples
           {:normal {:GT "1|0"}} [:normal]
@@ -50,13 +51,13 @@
              {:normal {:A [1]}} [:normal]
              {:A {:type "Integer" :number 2}})
             [:normal :A])
-           ["Invalid number of elements. Requires 2 , but 1."]))
+           ["Invalid number of elements. Requires 2, but got 1."]))
     (is (= (get-in
             (#'validator/check-each-samples
              {:normal {:A [1]} :alt ["A" "T"]} [:normal]
              {:A {:type "Integer" :number "A"}})
             [:normal :A])
-           ["Invalid number of elements. Requires A , but 1."])))
+           ["Invalid number of elements. Requires A, but got 1."])))
   (testing "not contain meta"
     (is (= (get-in
             (#'validator/check-each-samples